Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000651.1 Hibiscus syriacus cultivar Beakdansim tig00001258_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 87552
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:6263 original size:53 final size:54
Alignment explanation
Indices: 6178--6296 Score: 170
Period size: 53 Copynumber: 2.2 Consensus size: 54
6168 AAATGACTAA
* * *
6178 GGGTATCGGTACCTATCAGGCATTATGTTTTTCTCGGAGCCAAAATTGGCATAG
1 GGGTATCGGTACCCATCAGGCATTATGTTTTTCTCAGAGACAAAATTGGCATAG
*
6232 GGGTATCGGTACCCAT-TGGCATCT-TGTTTTTCTCAGAGACAAAATTGGCATAG
1 GGGTATCGGTACCCATCAGGCAT-TATGTTTTTCTCAGAGACAAAATTGGCATAG
*
6285 GGGTACCGGTAC
1 GGGTATCGGTAC
6297 ACCCTATGAG
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
53 43 0.73
54 16 0.27
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (54 bp):
GGGTATCGGTACCCATCAGGCATTATGTTTTTCTCAGAGACAAAATTGGCATAG
Found at i:6319 original size:22 final size:22
Alignment explanation
Indices: 6291--6340 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
6281 ATAGGGGTAC
6291 CGGTACACCCTATGAGGAGTAT
1 CGGTACACCCTATGAGGAGTAT
*
6313 CGGTACACCCTATGAGGGGTAT
1 CGGTACACCCTATGAGGAGTAT
6335 CGGTAC
1 CGGTAC
6341 CTCCTTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.24, C:0.24, G:0.30, T:0.22
Consensus pattern (22 bp):
CGGTACACCCTATGAGGAGTAT
Found at i:8955 original size:21 final size:19
Alignment explanation
Indices: 8905--9005 Score: 94
Period size: 21 Copynumber: 4.8 Consensus size: 19
8895 GTACCCTTAT
* *
8905 AGGGGTATCGATCACATTCAA
1 AGGGGTATCGAT-ACCTT-GA
8926 AGAGGGTATCGATACACGTTGA
1 AG-GGGTATCGATAC-C-TTGA
*
8948 AGGGGTATCGATACCTAGCA
1 AGGGGTATCGATACCTTG-A
8968 AGGGGGTATCGATACCTATGA
1 A-GGGGTATCGATACCT-TGA
8989 AGGGGGTATCGATACCT
1 A-GGGGTATCGATACCT
9006 AATGCATAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
19 2 0.03
20 3 0.04
21 49 0.70
22 14 0.20
23 2 0.03
ACGTcount: A:0.30, C:0.17, G:0.31, T:0.23
Consensus pattern (19 bp):
AGGGGTATCGATACCTTGA
Found at i:9006 original size:21 final size:21
Alignment explanation
Indices: 8929--9006 Score: 108
Period size: 21 Copynumber: 3.7 Consensus size: 21
8919 CATTCAAAGA
8929 GGGTATCGATACACGT-TGAA-G
1 GGGTATCGATAC-C-TATGAAGG
8950 GGGTATCGATACCTA-GCAAGG
1 GGGTATCGATACCTATG-AAGG
8971 GGGTATCGATACCTATGAAGG
1 GGGTATCGATACCTATGAAGG
8992 GGGTATCGATACCTA
1 GGGTATCGATACCTA
9007 ATGCATAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
19 2 0.04
20 3 0.06
21 47 0.89
22 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.32, T:0.23
Consensus pattern (21 bp):
GGGTATCGATACCTATGAAGG
Found at i:10600 original size:19 final size:19
Alignment explanation
Indices: 10576--10612 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
10566 TGAGTATAGC
10576 CTTGAGCAACAAGTCTAGG
1 CTTGAGCAACAAGTCTAGG
10595 CTTGAGCAACAAGTCTAG
1 CTTGAGCAACAAGTCTAG
10613 CCTTTTTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.22
Consensus pattern (19 bp):
CTTGAGCAACAAGTCTAGG
Found at i:15363 original size:54 final size:54
Alignment explanation
Indices: 15300--15412 Score: 165
Period size: 54 Copynumber: 2.1 Consensus size: 54
15290 TAAATGACTA
*
15300 GGGTATCGGTACCCATCAGGCAT-TCTATTTTACTCGGAGCCAAAATTGGCATAG
1 GGGTATCGGTACCCATCAGGCATCT-TATTTTACTCAGAGCCAAAATTGGCATAG
** * *
15354 GGGTATCGGTACCCATTTGGCATCTTGTTTTTCTCAGAGCCAAAATTGGCATAG
1 GGGTATCGGTACCCATCAGGCATCTTATTTTACTCAGAGCCAAAATTGGCATAG
15408 GGGTA
1 GGGTA
15413 CCAATACACC
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 52 0.98
55 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (54 bp):
GGGTATCGGTACCCATCAGGCATCTTATTTTACTCAGAGCCAAAATTGGCATAG
Found at i:16043 original size:2 final size:2
Alignment explanation
Indices: 16036--16060 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16026 TCAAAACCAA
16036 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
16061 AGCATCTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18090 original size:20 final size:21
Alignment explanation
Indices: 18063--18123 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
18053 AGATACACGT
18063 TGAA-GGGGTATCGATACCTA
1 TGAAGGGGGTATCGATACCTA
18083 -GCAAGGGGGTATCGATACCTA
1 TG-AAGGGGGTATCGATACCTA
18104 TGAAGGGGGTATCGATACCT
1 TGAAGGGGGTATCGATACCT
18124 GGTGCACAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
19 1 0.03
20 2 0.05
21 34 0.89
22 1 0.03
ACGTcount: A:0.28, C:0.16, G:0.33, T:0.23
Consensus pattern (21 bp):
TGAAGGGGGTATCGATACCTA
Found at i:23555 original size:73 final size:75
Alignment explanation
Indices: 23467--23630 Score: 215
Period size: 73 Copynumber: 2.2 Consensus size: 75
23457 TTAAATGACT
* *
23467 AGGGGTATCGGTACCCATAAGGCATTCTGTTTTTCTCGAAGCCAAAATTAGCATAGGGGTATCAG
1 AGGGGTATCGGTACCCATAAGACATTCTGTTTTTATCGAAGCCAAAATTAGCATAGGGGTATCAG
*
23532 -CACCCTGTG
66 ACACCCTATG
** * * * *
23541 A-GGGTATCGGTACCCATTTGACATTTTGTTTTTATCGGAGCCAAAATTTGCATAGGGGTATCGG
1 AGGGGTATCGGTACCCATAAGACATTCTGTTTTTATCGAAGCCAAAATTAGCATAGGGGTATCAG
23605 TACACCCTATG
66 -ACACCCTATG
*
23616 AGGGGTATCGATACC
1 AGGGGTATCGGTACC
23631 TCCTTATTTA
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
73 55 0.71
74 1 0.01
75 9 0.12
76 12 0.16
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (75 bp):
AGGGGTATCGGTACCCATAAGACATTCTGTTTTTATCGAAGCCAAAATTAGCATAGGGGTATCAG
ACACCCTATG
Found at i:32184 original size:19 final size:21
Alignment explanation
Indices: 32157--32196 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
32147 TTTTGTATTA
32157 CTATAATTATT-TA-ATTTTT
1 CTATAATTATTATATATTTTT
*
32176 CTATTATTATTATATATTTTT
1 CTATAATTATTATATATTTTT
32197 TTCCCTCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 2 0.11
21 6 0.33
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (21 bp):
CTATAATTATTATATATTTTT
Found at i:36249 original size:39 final size:39
Alignment explanation
Indices: 36178--36255 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
36168 CCCGGAATAT
* *
36178 TACCCGGGGACGCATCTGCTACTAAAGGGAAAGTAGCAC
1 TACCCGGGGACGCATCTGCTACCAAAGCGAAAGTAGCAC
* * *
36217 TACCCGGGGACTCA-CTCGTTACCAAAGCGAAAGTTGCAC
1 TACCCGGGGACGCATCT-GCTACCAAAGCGAAAGTAGCAC
36256 CTGCTGCGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
38 2 0.06
39 31 0.94
ACGTcount: A:0.29, C:0.28, G:0.26, T:0.17
Consensus pattern (39 bp):
TACCCGGGGACGCATCTGCTACCAAAGCGAAAGTAGCAC
Found at i:36378 original size:21 final size:21
Alignment explanation
Indices: 36332--36388 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
36322 ACTTTGATGA
*
36332 AGAAGATAAAGCTAAAAAGAT
1 AGAAGATAAAGATAAAAAGAT
* *
36353 GGAAGA-AAAGATAAAAATATT
1 AGAAGATAAAGATAAAAAGA-T
*
36374 AGAAGATCAA-ATAAA
1 AGAAGATAAAGATAAA
36389 GATGGTCCAG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 11 0.38
21 16 0.55
22 2 0.07
ACGTcount: A:0.63, C:0.04, G:0.18, T:0.16
Consensus pattern (21 bp):
AGAAGATAAAGATAAAAAGAT
Found at i:42947 original size:1 final size:1
Alignment explanation
Indices: 42941--42966 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
42931 TCCTAAGTTG
42941 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
42967 CGTTTGGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:43545 original size:1 final size:1
Alignment explanation
Indices: 43539--43564 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
43529 GAGCATCTTC
43539 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
43565 TCATCAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:44425 original size:105 final size:105
Alignment explanation
Indices: 43748--44417 Score: 1080
Period size: 105 Copynumber: 6.4 Consensus size: 105
43738 AGGTTTTACC
*
43748 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC-CATAGACAACGCAAGTTCAACTTCAC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC-CAGACAACGCAAGTTCAACTTCAC
*
43812 GACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCCAA-TT
65 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCT-CAATTT
*
43853 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC-CATAGACAACGCAAGTTCAACTTCAC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC-CAGACAACGCAAGTTCAACTTCAC
*
43917 GACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCCAA-TT
65 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCT-CAATTT
* *
43958 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACCCCAGACGACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
44023 ATGAAGGGACCGCTGGTTGTCACCAAACGTTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* * *
44063 CAGAGCCAATTTCAACCTCATAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
44128 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
44168 CAGAGCCAATTTCGACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * * *
44233 ACGAAGGGACCGCTGCTTGTCAAC-AACGACTTCCCAATCT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTT
44273 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
44338 ACGAAGGGACCGCCGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
44378 CAGAGCCAATCTCAACTTCACAACGAAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
44418 GAAACAACAC
Statistics
Matches: 532, Mismatches: 29, Indels: 8
0.93 0.05 0.01
Matches are distributed among these distances:
104 6 0.01
105 522 0.98
106 4 0.01
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:50691 original size:59 final size:59
Alignment explanation
Indices: 50610--50740 Score: 149
Period size: 59 Copynumber: 2.2 Consensus size: 59
50600 TTTGGTGACC
* ** *
50610 AATTTAGAATGAAGGTCCTAGTTTTGAGATGAAATTGAAATATTCAAAAATTTGAGGA-T
1 AATTTAGAATGAA-GTCCTAGTTTAGAGATGAAATCAAAATATTCAAAAATTTAAGGACT
* * *
50669 AATTTAGAATGATA-TCCATAGTTTAGGGATGAAATCAAAATATTTAAAAGTTTAAGGACT
1 AATTTAGAATGA-AGTCC-TAGTTTAGAGATGAAATCAAAATATTCAAAAATTTAAGGACT
*
50729 AATTTAAAATGA
1 AATTTAGAATGA
50741 GGATCATATT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
58 3 0.05
59 45 0.74
60 13 0.21
ACGTcount: A:0.44, C:0.05, G:0.18, T:0.34
Consensus pattern (59 bp):
AATTTAGAATGAAGTCCTAGTTTAGAGATGAAATCAAAATATTCAAAAATTTAAGGACT
Found at i:61715 original size:21 final size:22
Alignment explanation
Indices: 61680--61721 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
61670 GACCAACATT
*
61680 TTTGCATTCTTGCATTCGCATC
1 TTTGCATTCTTGCATTAGCATC
61702 TTTGCATT-TTGCATTAGCAT
1 TTTGCATTCTTGCATTAGCAT
61722 TTCACTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.17, C:0.21, G:0.14, T:0.48
Consensus pattern (22 bp):
TTTGCATTCTTGCATTAGCATC
Found at i:64201 original size:36 final size:36
Alignment explanation
Indices: 64134--64241 Score: 121
Period size: 36 Copynumber: 3.0 Consensus size: 36
64124 TCTCTTGAGG
**
64134 TTCGTCTCGCTCA-AGACGAGTTTTCGCAAAAACAAAT
1 TTCGTCTCGCT-AGAGAC-AGTTTTCTTAAAAACAAAT
* *
64171 TTTGTCTCGCTTGAGACAGTTTTCTTAAAAACAAAT
1 TTCGTCTCGCTAGAGACAGTTTTCTTAAAAACAAAT
* *
64207 TTCGTCTCGCTAGAGATAATTTTCCTT-AAAACAAA
1 TTCGTCTCGCTAGAGACAGTTTT-CTTAAAAACAAA
64242 ATTAATTATT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
36 44 0.72
37 17 0.28
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.33
Consensus pattern (36 bp):
TTCGTCTCGCTAGAGACAGTTTTCTTAAAAACAAAT
Found at i:64408 original size:65 final size:65
Alignment explanation
Indices: 64339--64467 Score: 197
Period size: 65 Copynumber: 2.0 Consensus size: 65
64329 AACAAAATTG
* * * *
64339 ATAAACTTTGAGATTG-TTTCTCTTGAAATAAATTTTGTCTCCCTTAAGACAGTTTCTCTTGAAA
1 ATAAACTTTGAGAATGTTTTC-CTTAAAACAAATTTTGTCTCCCTTAAGACAGTTTCCCTTGAAA
64403 A
65 A
*
64404 ATAAACTTTGAGAATGTTTTCCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAA
1 ATAAACTTTGAGAATGTTTTCCTTAAAACAAATTTTGTCTCCCTTAAGACAGTTTCCCTTGAAA
64468 CAAATTTTGT
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
65 54 0.93
66 4 0.07
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (65 bp):
ATAAACTTTGAGAATGTTTTCCTTAAAACAAATTTTGTCTCCCTTAAGACAGTTTCCCTTGAAAA
Found at i:64448 original size:21 final size:21
Alignment explanation
Indices: 64424--64507 Score: 99
Period size: 21 Copynumber: 4.3 Consensus size: 21
64414 AGAATGTTTT
*
64424 CCTTAAAACAAATTTTGTCTC
1 CCTTGAAACAAATTTTGTCTC
* *
64445 CCTTGAGAC--A-GTT-T--C
1 CCTTGAAACAAATTTTGTCTC
64460 CCTTGAAACAAATTTTGTCTC
1 CCTTGAAACAAATTTTGTCTC
64481 CCTTGAAACAAATTTTGTCTC
1 CCTTGAAACAAATTTTGTCTC
64502 CCTTGA
1 CCTTGA
64508 GATAGTTTCC
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
15 9 0.17
17 2 0.04
18 4 0.08
19 2 0.04
21 35 0.67
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.37
Consensus pattern (21 bp):
CCTTGAAACAAATTTTGTCTC
Found at i:64469 original size:36 final size:36
Alignment explanation
Indices: 64411--64486 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
64401 AAAATAAACT
*
64411 TTGAGAATGTTTTCCTTAAAACAAATTTTGTCTCCC
1 TTGAGAATGTTTCCCTTAAAACAAATTTTGTCTCCC
*
64447 TTGAGACA-GTTTCCCTTGAAACAAATTTTGTCTCCC
1 TTGAGA-ATGTTTCCCTTAAAACAAATTTTGTCTCCC
64483 TTGA
1 TTGA
64487 AACAAATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 36 0.97
37 1 0.03
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.39
Consensus pattern (36 bp):
TTGAGAATGTTTCCCTTAAAACAAATTTTGTCTCCC
Found at i:64517 original size:57 final size:60
Alignment explanation
Indices: 64424--64546 Score: 189
Period size: 57 Copynumber: 2.1 Consensus size: 60
64414 AGAATGTTTT
* * *
64424 CCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTG-AA-ACAA-ATTTTGTCTC
1 CCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTCGAAATAAAAGATTTTGTCTC
*
64481 CCTTGAAACAAATTTTGTCTCCCTTGAGATAGTTTCCCTCGAAATAAAAGATTTTGTCTC
1 CCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTCGAAATAAAAGATTTTGTCTC
64541 CCTTGA
1 CCTTGA
64547 GACAGTTTCC
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
57 38 0.64
58 2 0.03
59 3 0.05
60 16 0.27
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.37
Consensus pattern (60 bp):
CCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTCGAAATAAAAGATTTTGTCTC
Found at i:64519 original size:36 final size:36
Alignment explanation
Indices: 64479--64597 Score: 175
Period size: 36 Copynumber: 3.2 Consensus size: 36
64469 AAATTTTGTC
64479 TCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTT
1 TCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTT
* * *
64515 TCCCTCGAAATAAAAGATTTTGTCTCCCTTGAGACAGTT
1 TCCCTTG-AA-ACAA-ATTTTGTCTCCCTTGAGATAGTT
*
64554 TCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTC
1 TCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTT
64590 TCCCTTGA
1 TCCCTTGA
64598 GACAGTTTTC
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
36 35 0.48
37 5 0.07
38 5 0.07
39 28 0.38
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.36
Consensus pattern (36 bp):
TCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTT
Found at i:64639 original size:54 final size:51
Alignment explanation
Indices: 64536--64651 Score: 169
Period size: 54 Copynumber: 2.2 Consensus size: 51
64526 AAAAGATTTT
* *
64536 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATA
1 GTCTCCCTTGAGACAGTTTCCCTCGAAAAAAATTTTGTCTCCCTTGAGATA
*
64587 GTCTCCCTTGAGACAGTTTTCCTCGAAATAAAAGATTTTGTCTCCCTTGAGATA
1 GTCTCCCTTGAGACAGTTTCCCTCG-AA-AAAA-ATTTTGTCTCCCTTGAGATA
*
64641 GTTTCCCTTGA
1 GTCTCCCTTGA
64652 AACAAATTTT
Statistics
Matches: 58, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
51 23 0.40
52 2 0.03
53 3 0.05
54 30 0.52
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.36
Consensus pattern (51 bp):
GTCTCCCTTGAGACAGTTTCCCTCGAAAAAAATTTTGTCTCCCTTGAGATA
Found at i:64644 original size:90 final size:90
Alignment explanation
Indices: 64435--64684 Score: 383
Period size: 90 Copynumber: 2.7 Consensus size: 90
64425 CTTAAAACAA
* *
64435 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAAACAAATTTTGTC
1 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTG----AGA--TAGTC
*
64500 TCCCTTGAGATAGTTTCCCTCGAAATAAAAG
60 TCCCTTGAGACAGTTTCCCTCGAAATAAAAG
64531 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTCTCCCTT
1 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTCTCCCTT
*
64596 GAGACAGTTTTCCTCGAAATAAAAG
66 GAGACAGTTTCCCTCGAAATAAAAG
* * *
64621 ATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCT
1 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTCTCCCT
64685 CGAAATAAAT
Statistics
Matches: 147, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
90 94 0.64
92 2 0.01
96 51 0.35
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (90 bp):
ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTCTCCCTT
GAGACAGTTTCCCTCGAAATAAAAG
Found at i:64668 original size:36 final size:36
Alignment explanation
Indices: 64587--65178 Score: 630
Period size: 39 Copynumber: 15.9 Consensus size: 36
64577 CCTTGAGATA
* * *
64587 GTCTCCCTTGAGACAGTTTTCCTCGAAATAAAAGATTTT
1 GTCTCCCTTGAGACAGTTTCCCTTG-AA-ACAA-ATTTT
*
64626 GTCTCCCTTGAGATAGTTTCCCTTGAAACAAATTTT
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
* *
64662 GTCTCCCTTGAGACAGTTTCCCTCGAAATAAATGATTTT
1 GTCTCCCTTGAGACAGTTTCCCTTGAAA-CAA--ATTTT
64701 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
64737 GTCT-CCTTGAGACAGTTTCCCTTGAAACAAATTTT
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
*
64772 GTCTCCCTTGAGACAGTCTCCCTTGAAACAAATTTT
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
* *
64808 GTCTCCCTTGAGACAATTTCCCTTGAAACAAATTTA
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
* *
64844 GTTTCCCTTAAGACAGTTTCCCTTGAAACAAATTTT
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
* * *
64880 GTCTCCCTTGAGATAGTTTCCCTTAAAACAAATTTA
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
64916 GTCT-CCTTGAGACAGTTTCCCTTGAAACAAATTTT
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
* * *
64951 GTCTCCTTTGAGATAGTTTCCCTCGAAACAGAATAATTT
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACA-AAT--TTT
* * * *
64990 GTCTCGCTTGAGATAGTTTCACTTGAAATAAAAGATTTT
1 GTCTCCCTTGAGACAGTTTCCCTTG-AA-ACAA-ATTTT
* ** * * *
65029 ATCTTGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
1 GTCTCCCTTGAGACAGTTTCCCTTGAAAC--AA-ATTTT
* * * *
65068 GTCTCGCTTGAGATAGTTTCCTTTGAAACAAAAGATCTT
1 GTCTCCCTTGAGACAGTTTCCCTTGAAAC--AA-ATTTT
* * *
65107 GTCTCGCTTGAGATAGTTTCCCTCGAAACAGAATATTTT
1 GTCTCCCTTGAGACAGTTTCCCTTGAAAC--AA-ATTTT
* * * * *
65146 ATCTCACTTGAGATAGTTTCTCTCGAAACAAAT
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAAT
65179 GATTTTATAA
Statistics
Matches: 488, Mismatches: 52, Indels: 29
0.86 0.09 0.05
Matches are distributed among these distances:
35 67 0.14
36 194 0.40
37 11 0.02
38 6 0.01
39 203 0.42
40 3 0.01
41 4 0.01
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (36 bp):
GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
Found at i:64724 original size:15 final size:15
Alignment explanation
Indices: 64704--64761 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 15
64694 TGATTTTGTC
64704 TCCCTTGAGACAGTT
1 TCCCTTGAGACAGTT
* *
64719 TCCCTTGAAACAAATTTT
1 TCCCTTGAGAC--A-GTT
64737 GTCTCCTTGAGACAGTT
1 -TC-CCTTGAGACAGTT
64754 TCCCTTGA
1 TCCCTTGA
64762 AACAAATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
15 16 0.47
16 2 0.06
17 3 0.09
18 3 0.09
19 2 0.06
20 8 0.24
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.36
Consensus pattern (15 bp):
TCCCTTGAGACAGTT
Found at i:64780 original size:21 final size:21
Alignment explanation
Indices: 64754--64890 Score: 87
Period size: 21 Copynumber: 7.4 Consensus size: 21
64744 TGAGACAGTT
64754 TCCCTTGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
*
64775 TCCCTTGAGAC--A----GTC
1 TCCCTTGAAACAAATTTTGTC
64790 TCCCTTGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
*
64811 TCCCTTGAGAC-AA---T-T-
1 TCCCTTGAAACAAATTTTGTC
* *
64826 TCCCTTGAAACAAATTTAGTT
1 TCCCTTGAAACAAATTTTGTC
*
64847 TCCCTT-AAGAC--A----GTT
1 TCCCTTGAA-ACAAATTTTGTC
64862 TCCCTTGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
64883 TCCCTTGA
1 TCCCTTGA
64891 GATAGTTTCC
Statistics
Matches: 90, Mismatches: 6, Indels: 40
0.66 0.04 0.29
Matches are distributed among these distances:
15 34 0.38
16 5 0.06
17 3 0.03
19 2 0.02
20 5 0.06
21 41 0.46
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.36
Consensus pattern (21 bp):
TCCCTTGAAACAAATTTTGTC
Found at i:70926 original size:2 final size:2
Alignment explanation
Indices: 70919--70955 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
70909 CGTCCTCCAA
70919 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
70956 AGTAAGTTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:73807 original size:62 final size:62
Alignment explanation
Indices: 73728--73853 Score: 216
Period size: 62 Copynumber: 2.0 Consensus size: 62
73718 GCTATGTTTG
* * *
73728 TAAATGAATTGGGTTTGAACAAATAAATTTGTGTTTGTATTTCTTTGTTTACTTTTGAAGCA
1 TAAATGAATCGAGTTTGAACAAATAAACTTGTGTTTGTATTTCTTTGTTTACTTTTGAAGCA
*
73790 TAAATGAATCGAGTTTGAGCAAATAAACTTGTGTTTGTATTTCTTTGTTTACTTTTGAAGCA
1 TAAATGAATCGAGTTTGAACAAATAAACTTGTGTTTGTATTTCTTTGTTTACTTTTGAAGCA
73852 TA
1 TA
73854 CTCGTCCCAA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.45
Consensus pattern (62 bp):
TAAATGAATCGAGTTTGAACAAATAAACTTGTGTTTGTATTTCTTTGTTTACTTTTGAAGCA
Found at i:75674 original size:36 final size:36
Alignment explanation
Indices: 75634--75771 Score: 163
Period size: 36 Copynumber: 3.9 Consensus size: 36
75624 TAAGAAAAAT
* * *
75634 GAAAGAAAGCGTCGACACTTCCGATTCAAGTAGAAC
1 GAAAGGAAGCATCGACACTTCCGATTCAAGTCGAAC
*
75670 GAAAGGAAGCATCGGCACTTCCGATTCAAGTCGAAC
1 GAAAGGAAGCATCGACACTTCCGATTCAAGTCGAAC
* *
75706 GGAAGGAAGCATTGACACTTCCGATTCAAGTCGAAC
1 GAAAGGAAGCATCGACACTTCCGATTCAAGTCGAAC
* * * *
75742 -AGAAGGATGTATCG-CACTTTCGTTTCAAGT
1 GA-AAGGAAGCATCGACACTTCCGATTCAAGT
75772 GTTCATCTTT
Statistics
Matches: 88, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
35 14 0.16
36 74 0.84
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (36 bp):
GAAAGGAAGCATCGACACTTCCGATTCAAGTCGAAC
Found at i:80505 original size:44 final size:44
Alignment explanation
Indices: 80437--80562 Score: 198
Period size: 44 Copynumber: 2.9 Consensus size: 44
80427 TCTGACATGT
* * *
80437 CTGCGAACCAAACATAATATGGAATTAGATTTCAATTCTATTTC
1 CTGCCAACCAAACATAATATGGAATTGGATTACAATTCTATTTC
*
80481 CTGCCAACCAAACATAATATGGAATTGGATTCCAATTCTATTTC
1 CTGCCAACCAAACATAATATGGAATTGGATTACAATTCTATTTC
* *
80525 CTGCCAACCAAACAAAATATTGAATTGGATTACAATTC
1 CTGCCAACCAAACATAATATGGAATTGGATTACAATTC
80563 CTGACAGATT
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 76 1.00
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.31
Consensus pattern (44 bp):
CTGCCAACCAAACATAATATGGAATTGGATTACAATTCTATTTC
Found at i:83681 original size:45 final size:45
Alignment explanation
Indices: 83632--83719 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
83622 GAACATCGAA
* * *
83632 TGCATTTTATGCATCGATGCACATACCATGCATCGATGTACTCAG
1 TGCATTTGATGCATCGATGCACAAACCATGCATCGATGCACTCAG
83677 TGCATTTGATGCATCGATGCACAAACCATGCATCGATGCACTC
1 TGCATTTGATGCATCGATGCACAAACCATGCATCGATGCACTC
83720 TGGCTATTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.28
Consensus pattern (45 bp):
TGCATTTGATGCATCGATGCACAAACCATGCATCGATGCACTCAG
Done.